Merge branch 'devel'

.gitignore

@@ -1,7 +1,16 @@
+*/Makefile.in
 Makefile.in
 aclocal.m4
-configure
-*/Makefile.in
 autom4te.cache
+config/
+configure
+docs/*.aux
+docs/*.log
+docs/*.pdf
+docs/ref/html
+docs/ref/qdptags
+docs/ref/warnings
+docs/usr/html
+docs/usr/warnings
 include/qdp_config_internal.h.in
 include/qdp_config_internal.h.in~

.gitmodules

@@ -1,12 +1,12 @@
 [submodule "other_libs/libintrin"]
 	path = other_libs/libintrin
-	url = git@github.com:usqcd-software/libintrin.git
+	url = ../libintrin.git
 [submodule "other_libs/xpath_reader"]
 	path = other_libs/xpath_reader
-	url = git@github.com:usqcd-software/xpath_reader.git
+	url = ../xpath_reader.git
 [submodule "other_libs/qio"]
 	path = other_libs/qio
-	url = git@github.com:usqcd-software/qio.git
+	url = ../qio.git
 [submodule "other_libs/filedb"]
 	path = other_libs/filedb
-	url = git@github.com:usqcd-software/filedb.git
+	url = ../filedb.git

FindQDPXX.cmake.in

@@ -0,0 +1,87 @@
+set( QDPXX_INSTALL_DIR "@prefix@" )
+set( QDPXX_PARALLEL_ARCH "@CONFIG_PARALLEL_ARCH@" )
+set( QDPXX_INCLUDE_DIR "@prefix@/include" )
+set( QDPXX_LIBDIR "@prefix@/lib")
+
+# Get the Include directories out of the CFLAGS Line if they start with -I
+string(STRIP "@HDF5_CXXFLAGS@ @LIBXML2_CXXFLAGS@ @QMP_CFLAGS@ @QMT_CXXFLAGS@" BASE_EXTRA_CXXFLAGS)
+
+# Match all strings which start with -I and keep matching anything until we reach another '-'
+# [^-] means match everything other than - and the + means do this one or more times.
+#
+string(REGEX MATCHALL  "\\-\\I[^-]+" BASE_EXTRA_INCLUDES ${BASE_EXTRA_CXXFLAGS})
+
+# Replace "-I" (ie \-\I ) with nothing
+string(REGEX REPLACE "\\-\\I" "" EXTRA_INCLUDE_DIRS ${BASE_EXTRA_INCLUDES})
+separate_arguments(${EXTRA_INCLUDE_DIRS})
+
+# Find the library we built and add it as an imported target
+# with appropriate include dir and location
+function(add_qdpxx_lib LIBNAME)
+ message(STATUS "Libname: ${LIBNAME}")
+
+ # This will find the file, whether a .so or a .a appropriately
+ find_library(LIB_${LIBNAME} NAMES ${LIBNAME} PATHS "${QDPXX_LIBDIR}")
+
+ # Set up the library as an imported target
+ add_library(${LIBNAME} UNKNOWN IMPORTED )
+
+ # Explain where it is
+ set_target_properties(${LIBNAME} PROPERTIES IMPORTED_LOCATION ${LIB_${LIBNAME}})
+ # Set the include dir
+ set_target_properties(${LIBNAME} PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${QDPXX_INCLUDE_DIR}")
+endfunction()
+
+# Toplevel QDP++ library
+add_qdpxx_lib(qdp)
+# Add on Extra includes
+foreach( INCDIR ${EXTRA_INCLUDE_DIRS})
+ message(STATUS "Adding ${INCDIR}")
+ set_target_properties(qdp PROPERTIES INTERFACE_INCLUDE_DIRECTORIES ${INCDIR})       
+endforeach()
+
+
+
+# XML Reader and writer
+add_qdpxx_lib(XPathReader)
+add_qdpxx_lib(xmlWriter)
+target_link_libraries(qdp INTERFACE XPathReader xmlWriter)
+
+# QIO and LIME
+add_qdpxx_lib(lime)
+add_qdpxx_lib(qio)
+target_link_libraries(qio INTERFACE lime)
+target_link_libraries(qdp INTERFACE qio)
+
+# Check if using LibIntrin 
+string(STRIP "@LIBINTRIN_DIR@" QDPXX_LIBINTRIN)
+if( QDPXX_LIBINTRIN )
+  add_qdpxx_lib(intrin)
+  target_link_libraries(qdp INTERFACE intrin)
+endif()
+
+# Check if using FILEDB
+string(STRIP "@FILEDB_DIR" QDPXX_FILEDB)
+if( QDPXX_FILEDB ) 
+   add_qdpxx_lib(filehash)
+   add_qdpxx_lib(filedb)
+   target_link_libraries(filedb INTERFACE filehash)
+   target_link_libraries(qdp INTERFACE filedb)
+endif()
+
+# Add other LFlags and libs which we didn't build
+string(STRIP "@LDFLAGS@ @HDF5_LDFLAGS@ @QMP_LDFLAGS@ @QMT_LDFLAGS@" QDPXX_LDFLAGS)
+string(STRIP "@HDF5_LIBS@ @LIBXML2_LIBS@ @QMP_LIBS@ @LIBS@ @QMT_LIBS@" QDPXX_LIBS)
+
+if( QDPXX_LDFLAGS ) 
+  separate_argumnets(${QDPXX_LDFLAGS})
+  target_link_options(qdp INTERFACE ${QDPXX_LDFLAGS})
+endif()
+
+if( QDPXX_LIBS )
+  separate_arguments(${QDPXX_LIBS})
+  target_link_libraries(qdp INTERFACE ${QDPXX_LIBS})
+endif()
+
+set( QDPXX_FOUND TRUE)
+

INSTALL

@@ -12,8 +12,8 @@ without warranty of any kind.
 Basic Installation
 ==================
 
-   Briefly, the shell command `./configure && make && make install'
-should configure, build, and install this package.  The following
+   Briefly, the shell commands `./configure; make; make install' should
+configure, build, and install this package.  The following
 more-detailed instructions are generic; see the `README' file for
 instructions specific to this package.  Some packages provide this
 `INSTALL' file but do not implement all of the features documented

LICENSE

@@ -0,0 +1,55 @@
+Jefferson Science Associates LLC Copyright Notice:
+
+Copyright � 2014 Jefferson Science Associates LLC All Rights Reserved.
+
+
+Redistribution and use in source and binary forms, with or without modification, are permitted as a licensed user provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+
+3. The name of the author may not be used to endorse or promote products derived from this software without specific prior written permission.
+
+This material resulted from work developed under a United States Government
+Contract.  The Government retains a paid-up, nonexclusive, irrevocable worldwide license in such copyrighted data to reproduce, distribute copies to the public, prepare derivative works, perform publicly and display publicly and to permit others to do so.  
+THIS SOFTWARE IS PROVIDED BY JEFFERSON SCIENCE ASSOCIATES LLC "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.  IN NO EVENT SHALL JEFFRSON SCIENCE ASSOCIATES, LLC OR THE U.S. GOVERNMENT BE LIABLE TO LICENSEE OR ANY THIRD PARTES FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+
+				COPYRIGHT AND LICENSE
+
+Copyright (c) 1995,1996   Southeastern Universities Research Association
+		          Continuous Electron Beam Accelerator Facility
+			  Thomas Jefferson National Accelerator Facility
+			  12000 Jefferson Avenue, Newport News, VA 23606 
+
+This material resulted from work developed under a United States Government 
+Contract and is subject to the following license:
+
+The Government retains a paid-up, nonexclusive, irrevocable worldwide license
+to reproduce, prepare derivative works, perform publicly and display publicly
+by or for the Government including the right to distribute to other Government
+contractors. 
+
+
+                  DISCLAIMER AND LIMITATION OF WARRANTY.                    
+
+         ALL SOFTWARE IS PROVIDED "AS IS" WITHOUT WARRANTY. THERE           
+         ARE NO WARRANTIES EXPRESS OR IMPLIED, INCLUDING ANY IMPLIED        
+         WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR            
+         PURPOSE. THERE IS NO WARRANTY THAT USE WILL NOT INFRINGE           
+         ANY PATENT, COPYRIGHT OR TRADEMARK.                                
+
+In consideration of the use of the software and other materials, user agrees
+that neither the Government nor SURA/TJNAF will be liable for any damages with 
+respect to such use, and user shall hold both the Government and SURA/TJNAF
+harmless from and indemnify them against any and all liability for damages
+arising out of the use of such software and other materials. In no event shall
+the Government or SURA/TJNAF be liable whether arising under contract, tort,
+strict liability or otherwise for any incidental, indirect or consequential 
+loss or damage of any nature arising at any time from any cause whatsoever. In
+addition, the Government and SURA/TJNAF assume no obligation for defending
+against third party claims or threats of claims arising as a result of user's
+use of the software or materials either as delivered to user or as modified by
+user.  
+

Makefile.am

@@ -10,7 +10,9 @@ SUBDIRS = lib examples include other_libs tests
 # 
 bin_SCRIPTS=qdp++-config
 
+dist_data_DATA = FindQDPXX.cmake
 #
 # Some things that we want in the distribution tarball 
 #
-EXTRA_DIST = PETE/QDPClasses.in PETE/QDPOps.in  PETE/Tools docs  install_scripts
+EXTRA_DIST = PETE/QDPClasses.in PETE/QDPOps.in  PETE/Tools docs  install_scripts FindQDPXX.cmake.in
+

NEWS

@@ -1,3 +1,11 @@
+05/10/2017 -- Balint Joo
+	Updated Memory allocators -- These are allocated using Singleton CreateStatic, 
+	and not destroyed (NoDestroy policy) -- Chroma staggered regressions now pass.
+       Some  Chroma regression tests currently fail with ICC-17 update 2 (parallel studio 2017.2.050)
+	Tests passed with icc-16 update 3 and gcc versions 5.3.0 and 6.2.0 - so treating this as a compiler bug for now.
+	BEWARE !!!!!
+
+
 02/06/2015 -- Balint Joo 
 	Updated submodules, pulled in HDF5 fixes (Thorsten Kurth)
         Added  Blue Gene Thread binding (orig. developed in QPhiX by Diptorup Deb)

PETE/QDPOps.in

@@ -373,6 +373,16 @@ binaryOps
   @return (real(trace(adj(l)*r))
   @ingroup group1
   @relates QDPType */"
+-----
+  TAG = "FnLocalColorInnerProduct"
+  FUNCTION = "localColorInnerProduct"
+  EXPR = "return (localColorInnerProduct(a,b));"
+  COMMENTA = "//! InnerProduct on only color fiber indices"
+  COMMENTB = "/*! L2 norm only color fiber indices
+  @sa adj(), trace()
+  @return (traceColor(adj(l)*r)
+  @ingroup group1
+  @relates QDPType */"
 -----
   TAG = "FnQuarkContract13"
   FUNCTION = "quarkContract13"

config/missing

@@ -1,7 +1,7 @@
 #! /bin/sh
 # Common wrapper for a few potentially missing GNU programs.
 
-scriptversion=2013-10-28.13; # UTC
+scriptversion=2012-06-26.16; # UTC
 
 # Copyright (C) 1996-2014 Free Software Foundation, Inc.
 # Originally written by Fran,cois Pinard <pinard@iro.umontreal.ca>, 1996.
@@ -160,7 +160,7 @@ give_advice ()
       ;;
    autom4te*)
       echo "You might have modified some maintainer files that require"
-      echo "the 'autom4te' program to be rebuilt."
+      echo "the 'automa4te' program to be rebuilt."
       program_details 'autom4te'
       ;;
     bison*|yacc*)

configure.ac

@@ -192,6 +192,26 @@ AC_ARG_ENABLE(bgq-thread-binding,
      [ ac_bgq_bind_enabled="no"]
 )
 
+AC_ARG_ENABLE(tbb-pool-allocator,
+	AC_HELP_STRING([--enable-tbb-pool-allocator],
+		[ Enable Threaded Building Blocks Fixed Pool Allocator]),
+	[ ac_enable_tbbpool=${enableval} ],
+	[ ac_enable_tbbpool="no" ]
+)
+
+AC_ARG_ENABLE(extramessages,
+   AC_HELP_STRING(
+    [--enable-extra-messages],
+    [Emit extra messages during the compilation that indicate which preprocessor branches are used]
+   ),
+   [ extra_messages_enabled="yes" ],
+   [ extra_messages_enabled="no" ]
+)
+
+if test "${extra_messages_enabled}" = "yes"; then
+	AC_MSG_NOTICE([Will emit pragma message ])
+	AC_DEFINE(QPHIX_EMIT_MESSAGES, [1], [ Emit compilation messages ])
+fi
 
 if test "X${ac_bgq_bind_enabled}X" = "XyesX";
 then
@@ -674,6 +694,14 @@ then
 	AC_DEFINE([QDP_USE_OMP_THREADS], [1], [ Use OpenMP Threads ])
 fi
 
+dnl Threaded Building Blocks Pool Allocator
+if test "X${ac_enable_tbbpool}X" == "XyesX";
+then 
+	AC_MSG_NOTICE([Configuring to use TBB Fixed Pool. Please ensure CXXFLAGS and LDFLAGS are correctly set])
+	AC_DEFINE([QDP_USE_TBBPOOL_ALLOCATOR],[1], [ Use TBB Fixed Pool Allocator ])
+fi
+
+
 dnl
 dnl
 dnl Now have all the options... Do some configuration 
@@ -703,6 +731,9 @@ AM_CONDITIONAL(BUILD_WILSON_EXAMPLES,
 AM_CONDITIONAL(BUILD_DEFAULT_ALLOCATOR,
   [test "X0X" = "X0X"])
 
+AM_CONDITIONAL(BUILD_QDPXX_TBB_ALLOCATOR,
+  [ test "X${ac_enable_tbbpool}X" == "XyesX" ])
+
 #
 # Conditional for use qmt
 #
@@ -786,6 +817,7 @@ fi
 #
 AC_CONFIG_FILES(Makefile)
 AC_CONFIG_FILES(qdp++-config)
+AC_CONFIG_FILES(FindQDPXX.cmake)
 AC_CONFIG_FILES(lib/Makefile)
 AC_CONFIG_FILES(other_libs/Makefile)
 AC_CONFIG_FILES(include/Makefile)

examples/t_basic.cc

@@ -46,6 +46,8 @@ int main(int argc, char *argv[])
   LatticeFermion    lftmp1;
   LatticeFermion    lftmp2;
   LatticeFermion    lftmp3;
+  LatticeColorVectorSpinMatrix lcvsp1;
+  LatticeColorVectorSpinMatrix lcvsp2;
   LatticeReal R1;
   LatticeReal Rtmp;
   LatticeComplex c;
@@ -147,7 +149,7 @@ int main(int argc, char *argv[])
   pop(xml_out);
 
 
-#if 0
+#if 1
 
   mu = 0;
   nu = 1;
@@ -181,7 +183,7 @@ int main(int argc, char *argv[])
   pop(xml_out);
 
   /* test 5 */
-  rtmp = real(trace(lctmp1 * u));
+  LatticeReal rtmp = real(trace(lctmp1 * u));
   push(xml_out,"TRACE_MULTIPLY_MATRIX_realpart");
   write(xml_out, "rtmp", rtmp);
   pop(xml_out);
@@ -391,7 +393,7 @@ int main(int argc, char *argv[])
 
   /* test 27 */
   gaussian(lqtmp1);
-  r = real(trace(adj(q) * lqtmp1));
+  LatticeReal r = real(trace(adj(q) * lqtmp1));
   push(xml_out,"TRACE_MULT_PROP");
   write(xml_out, "r", r);
   pop(xml_out);
@@ -406,6 +408,33 @@ int main(int argc, char *argv[])
   write(xml_out, "lqtmp24", quarkContract24(lqtmp1, lqtmp2));
   pop(xml_out);
 
+#if 1
+  /* test 29 */
+  gaussian(lcvsp1);
+  gaussian(lcvsp2);
+  //LatticeSpinMatrix spm = localColorInnerProduct(lcvsp1, lcvsp2);
+  auto spm = localColorInnerProduct(lcvsp1, lcvsp2);
+  push(xml_out,"LOCAL_COLOR_INNER_PRODUCT");
+  write(xml_out, "spm", spm);
+  pop(xml_out);
+
+  /* test 30 */
+  gaussian(lcvsp1);
+  gaussian(lcvsp2);
+  multi1d<SpinMatrixD> fred1 = sumMulti(spm, QDP::rb);
+  push(xml_out,"SUMMULTI_LOCAL_COLOR_INNER_PRODUCT1");
+  write(xml_out, "fred1", fred1);
+  pop(xml_out);
+
+  /* test 31 */
+  gaussian(lcvsp1);
+  gaussian(lcvsp2);
+  multi1d<SpinMatrixD> fred2 = sumMulti(localColorInnerProduct(lcvsp1, lcvsp2), QDP::rb);
+  push(xml_out,"SUMMULTI_LOCAL_COLOR_INNER_PRODUCT2");
+  write(xml_out, "fred2", fred2);
+  pop(xml_out);
+#endif
+
 #endif